- Contemporary messages sorted: [ by date ] [ by thread ] [ by subject ] [ by author ] [ by messages with attachments ]

From: Praneeth Bommisetti <iampraneeth11.gmail.com>

Date: Thu, 29 Sep 2016 11:33:25 +0530

Hello all,

I am trying to calculate the h-bond life time using the h-bond command

in cpptraj of Amber 14.

Command I used

*hbond out hbd2l.out donormask :2-22 acceptormask :1&!.H avgout hbd2l.dat

series *

Output looked something like this

#Acceptor DonorH Donor Frames Frac

AvgDist AvgAng

MOL_1.O3 DG5_2.HO5' DG5_2.O5' 30506 0.6101

2.7374 160.0488

MOL_1.O1 DC_11.H42 DC_11.N4 22038 0.4408

2.8489 160.2850

MOL_1.O1 DC_11.H41 DC_11.N4 7040 0.1408

2.8204 157.7933

MOL_1.N6 DG_13.H22 DG_13.N2 3242 0.0648

2.9357 154.6688

.

.

.

I assumed the fraction to be the life time. That means 0.61 implies 61% of

total frames

To verify this, alternatively I calculated the distance between atoms and

angles separately using cpptraj. Then, using excel, I made an adjoint set

where the dist<3.0 and angle>135 which are defaults. But then the

percentage of frames that satisfy these conditions exceeded significantly

compared to the fraction given by cpptraj. Also the average angle and avg

distance didn't match.

Any idea on how these disparities are coming ?

Any help would be appreciated.

Thanks

Date: Thu, 29 Sep 2016 11:33:25 +0530

Hello all,

I am trying to calculate the h-bond life time using the h-bond command

in cpptraj of Amber 14.

Command I used

*hbond out hbd2l.out donormask :2-22 acceptormask :1&!.H avgout hbd2l.dat

series *

Output looked something like this

#Acceptor DonorH Donor Frames Frac

AvgDist AvgAng

MOL_1.O3 DG5_2.HO5' DG5_2.O5' 30506 0.6101

2.7374 160.0488

MOL_1.O1 DC_11.H42 DC_11.N4 22038 0.4408

2.8489 160.2850

MOL_1.O1 DC_11.H41 DC_11.N4 7040 0.1408

2.8204 157.7933

MOL_1.N6 DG_13.H22 DG_13.N2 3242 0.0648

2.9357 154.6688

.

.

.

I assumed the fraction to be the life time. That means 0.61 implies 61% of

total frames

To verify this, alternatively I calculated the distance between atoms and

angles separately using cpptraj. Then, using excel, I made an adjoint set

where the dist<3.0 and angle>135 which are defaults. But then the

percentage of frames that satisfy these conditions exceeded significantly

compared to the fraction given by cpptraj. Also the average angle and avg

distance didn't match.

Any idea on how these disparities are coming ?

Any help would be appreciated.

Thanks

-- *Regards, * *Praneeth Bommisetti, * *Fourth year Undergraduate,* *Integrated M.Sc Chemistry, * *Indian Institute of Technology Bombay.* *T: +918424815358, id:praneeth.b.iitb.ac.in <id%3Apraneeth.b.iitb.ac.in>* _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Wed Sep 28 2016 - 23:30:02 PDT

Custom Search